Difference between revisions of "2016 AMBER tutorial with Thrombin"
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===MM-GBSA Energy Calculation=== | ===MM-GBSA Energy Calculation=== | ||
==V. Frequently Encountered Problems== | ==V. Frequently Encountered Problems== | ||
Revision as of 13:16, 6 April 2016
For additional Rizzo Lab tutorials see AMBER Tutorials.
In this tutorial, we will learn how to run a molecular dynamics simulation of a protein-ligand complex. We will then post-process that simulation by calculating structural fluctuations (with RMSD) and free energies of binding (MM-GBSA).
Contents
I. Introduction
Yaping
II. Structural Preparation
Antechamber, Parmchk, tLeap
Omar, Katie
III. Simulation using pmemd
PMEMD
Agatha, Haoyue
IV. Simulation Analysis
Ptraj
Lauren, Haoyue
